Variant report

Variant	rs2366774
Chromosome Location	chr5:89939067-89939068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89823962..89827222-chr5:89937926..89943647,5	K562	blood:
2	chr5:89938091..89940489-chr5:89979242..89981079,3	K562	blood:
3	chr5:89703250..89710229-chr5:89936398..89944611,13	K562	blood:
4	chr5:89701624..89708275-chr5:89936212..89939090,6	K562	blood:
5	chr5:89823998..89826895-chr5:89936976..89941414,5	K562	blood:
6	chr5:81571577..81575339-chr5:89936879..89939995,3	K562	blood:
7	chr5:89938077..89942103-chr5:90675427..90679817,6	K562	blood:
8	chr5:89938651..89940282-chr5:89943212..89946172,3	MCF-7	breast:
9	chr5:89897975..89900696-chr5:89937499..89939734,2	K562	blood:
10	chr5:89938681..89942307-chr5:90675773..90680271,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000153140	Chromatin interaction
ENSG00000186468	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000205464	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10036980	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs10043836	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10058765	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs10060427	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs10062714	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs10062924	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs10067181	0.84[JPT][hapmap]
rs10068473	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10072105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1028191	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1028192	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1033290	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10473936	0.82[ASN][1000 genomes]
rs10514327	0.81[CHB][hapmap]
rs10514333	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs10942597	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10942605	0.83[JPT][hapmap]
rs10942606	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs1160121	0.83[JPT][hapmap]
rs11741740	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12187830	0.88[ASN][1000 genomes]
rs12188928	0.83[JPT][hapmap]
rs12516985	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs13185955	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1533603	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs1673378	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1673379	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16868957	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs1700510	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs1700511	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1878878	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs1988788	0.86[ASN][1000 genomes]
rs1993474	0.83[JPT][hapmap]
rs2176624	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs2222242	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs2366771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2366773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366777	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28517617	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28550273	0.92[ASN][1000 genomes]
rs3805483	0.81[CHB][hapmap]
rs3927265	0.85[CHB][hapmap]
rs4379236	0.92[ASN][1000 genomes]
rs4574581	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474800	0.84[ASN][1000 genomes]
rs490812	0.92[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs491241	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916681	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs4916682	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916684	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916686	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs4916813	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916814	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916815	0.82[JPT][hapmap]
rs498491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs499148	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs501640	0.81[ASN][1000 genomes]
rs502596	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs552314	0.84[ASN][1000 genomes]
rs587818	0.80[ASN][1000 genomes]
rs603015	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs617379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs618355	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs623761	0.84[ASN][1000 genomes]
rs637442	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6452906	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs645652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648430	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs666659	0.82[ASN][1000 genomes]
rs6861525	0.85[ASN][1000 genomes]
rs6863710	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870337	0.83[ASN][1000 genomes]
rs6878917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881412	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs6883872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs688956	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs688960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6891275	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6898209	1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7703530	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7703588	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7721198	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs7723259	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs7724806	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs7726624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7729703	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7732169	0.83[JPT][hapmap]
rs9283788	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9293550	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs963866	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs977906	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs9790907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2366774	LYSMD3	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89918000-89950600	Weak transcription	Pancreas	Pancrea
2	chr5:89928800-89940000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:89928800-89941000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:89929000-89940400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:89929000-89948600	Weak transcription	Brain Anterior Caudate	brain
6	chr5:89934200-89939800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:89935800-89940000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:89935800-89941400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:89936600-89940800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:89936600-89940800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:89936600-89949000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:89936600-89951000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:89936800-89940800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:89936800-89941200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr5:89936800-89948600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:89936800-89951000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:89936800-89994200	Weak transcription	Brain Germinal Matrix	brain
18	chr5:89937000-89940400	Active TSS	K562	blood
19	chr5:89937000-89948600	Weak transcription	Fetal Brain Female	brain
20	chr5:89937200-89943000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:89937800-89940200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:89937800-89941000	Weak transcription	HSMM	muscle
23	chr5:89938000-89940000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:89938200-89939600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:89938200-89940200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:89938200-89940400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:89938400-89940000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:89938400-89940000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:89938400-89941400	Enhancers	Primary hematopoietic stem cells	blood
30	chr5:89938600-89939600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:89938600-89939800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:89938600-89941400	ZNF genes & repeats	GM12878-XiMat	blood
33	chr5:89938800-89939400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr5:89939000-89940000	Weak transcription	Primary monocytes fromperipheralblood	blood

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